Resource File Formats¶

This chapter describes the various files fastr uses. The function and format of the files is described allowing the user to configure fastr and add DataTypes and Tools.

Config file¶

Fastr reads the config files from the following locations by default (in order):

$FASTRHOME/config.py
~/.fastr/config.py

Reading a new config file change or override settings, making the last config file read have the highest priority. All settings have a default value, making config files and all settings within optional.

Example config file¶

Here is a minimal config file:

# Enable debugging output
debug = False

# Define the path to the tool definitions
tools_path = ['/path/to/tools',
              '/path/to/other/tools'] + tools_path
types_path = ['/path/to/datatypes',
              '/path/to/other/datatypes'] + types_path


# Specify what your preferred output types are.
preferred_types += ["NiftiImageFileCompressed",
                    "NiftiImageFile"]

# Set the tmp mount
mounts['tmp'] = '/path/to/tmpdir'

Format¶

The config file is actually a python source file. The next syntax applies to setting configuration values:

# Simple values
float_value = 1.0
int_value = 1
str_value = "Some value"
other_str_value = 'name'.capitalize()

# List-like values
list_value = ['over', 'ride', 'values']
other_list_value.prepend('first')
other_list_value.append('list')

# Dict-like values
dict_value = {'this': 1, 'is': 2, 'fixed': 3}
other_dict_value['added'] = 'this key'

Note

Dictionaries and list always have a default, so you can always append or assign elements to them and do not have to create them in a config file. Best practice is to only edit them unless you really want to block out the earliers config files.

Most operations will be assigning values, but for list and dict values a special wrapper object is used that allows manipulations from the default. This limits the operations allowed.

List values in the config.py have the following supported operators/methods:

+, __add__ and __radd__
+= or __iadd__
append
prepend
extend

Mapping (dict-like) values in the config.py have the following supported operators/methods:

update
[] or __getitem__, __setitem__ and __delitem__

Configuration fields¶

This is a table the known config fields on the system:

`Tool` description¶

Tools are the building blocks in the fastr network. To add new Tools to fastr, XML/json files containing a Tool definition can be added. These files have the following layout:

Attribute			Description
`id`			The id of this Tool (used internally in fastr)
`name`			The name of the Tool, for human readability
`version`			The version of the Tool wrapper (not the binary)
`url`			The url of the Tool wrapper
`authors[]`			List of authors of the Tools wrapper
	`name`		Name of the author
	`email`		Email address of the author
	`url`		URL of the website of the author
`tags`	`tag[]`		List of tags describing the Tool
`command`			Description of the underlying command
	`version`		Version of the tool that is wrapped
	`url`		Website where the tools that is wrapped can be obtained
	`targets[]`		Description of the target binaries/script of this Tool
		`os`	OS targeted (windows, linux, macos or * (for any)
		`arch`	Architecture targeted 32, 64 or * (for any)
		…	Extra variables based on the target used, see Targets
	`description`		Description of the Tool
	`license`		License of the Tool, either full license or a clear name (e.g. LGPL, GPL v2)
	`authors[]`		List of authors of the Tool (not the wrapper!)
		`name`	Name of the authors
		`email`	Email address of the author
		`url`	URL of the website of the author
`interface`			The interface definition see Interfaces
`help`			Help text explaining the use of the Tool
`cite`			Bibtext of the Citation(s) to reference when using this Tool for a publication